You can tell Hero Lab to use different "dataroot" (game system data) and "userroot" (default for saved characters) folders using command line options. It requires a bit of work to set up and breaks integration with Realm Works, so you may not want to use the feature, but it is there.

You can read about it in the Hero Lab manual: Open a game system in Hero Lab, go to Help/Hero Lab Manual, scroll down and pick Miscellaneous Details, and look for the Folder Locations section.